We have developed a novel method for efficiently screening affinity ligands (aptamers) against cancer biomarker proteins Shp2 [1] from a complex single-stranded DNA (ssDNA)library by employing single molecule emulsion PCR based on the agarose droplet microfluidic technology [2].SELEX (system evolution of ligands by exponential enrichment) method [3,4] is an in vitro conventional aptamer screening technique, which involves progressive selection of aptamers by repeated rounds of partitioning and amplification from a combinatorial oligonucleotide library.